hotspotter.variable: Find hotspots of genomic events

Description Usage Arguments Details Value Author(s)

View source: R/hotspotter.R

Description

Find hotspots of genomic events by using kernel density estimation.

Usage

1
hotspotter.variable(breakpoints, confint, pval = 0.05, spacing.bp = 5000)

Arguments

breakpoints

A list with GRanges-class object containing the coordinates of the genomic events and their confidence intervals.

confint

Confidence interval that was used for breakpoint estimation.

pval

P-value cutoff for hotspots.

spacing.bp

Spacing of datapoints for KDE in basepairs.

Details

The hotspotter uses a gaussian kernel with variable bandwidth to perform a KDE. The bandwidth depends on the confidence intervals of the breakpoints. A p-value is calculated by comparing the density profile of the genomic events with the density profile of a randomly subsampled set of genomic events (bootstrapping).

Value

A list of GRanges-class objects containing 1) coordinates of hotspots and 2) p-values within the hotspot.

Author(s)

Aaron Taudt


ataudt/aneufinder documentation built on Nov. 21, 2018, 10:10 a.m.